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#1105 - 03/23/04 11:14 AM very new to CHARMM
vani Offline
Forum Member

Registered: 03/23/04
Posts: 4
Hello:

I am new to CHARMM, and i have some questions regarding very basic operations.

1. Can CHARMM read coordinates from PDB files?
2. can anybody send me a script to do the following?
read the file from PDB
create PSF file.
3. Should the residues be listed, even if the coordinates are read from the PDB file?
4. should any lines be removed from the PDB file? or what iam trying to ask is what is the acceptable form of a PDB file?

Thanks

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#1106 - 03/23/04 11:37 AM Re: very new to CHARMM [Re: vani]
dsingh Offline
Forum Member

Registered: 11/12/03
Posts: 23
Loc: San Diego, CA
Vani,

I strongly recommend that you take a look at the script archive to get an idea of essential CHARMM commands and basic I/O. The first script I would look at for your questions is gen-prot.inp. This describes reading in a pdb file and generating a psf in some detail.

Good luck!!
_________________________
"Violence is the last refuge of the incompetent" -- Salvor Hardin Accelrys CHARMm User Group Meetings

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#1107 - 03/24/04 12:09 PM Re: very new to CHARMM [Re: vani]
jmwict13 Offline
Forum Member

Registered: 11/14/03
Posts: 36
Loc: W. Lafayette, IN USA
A few websites I looked at when I first got started that explain things in more detail than just staring at the docs and other peoples' scripts:

http://pekoe.chem.ukans.edu/~kuczera/Public/web/html/tasks/node1.html

http://www.psc.edu/general/software/packages/charmm/tutorial/index.html

Good Luck!
_________________________
Joshua Ward Graduate Student Purdue University Department of Medicinal Chemistry and Pharmacology

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